Regardless of location, all rhabdoid tumours are highly aggressive, have a poor prognosis, and tend to occur in children less than two years of age.

The standard work-up for AT/RT includes:

- Magnetic resonance imaging (MRI) of the brain and spine

- Lumbar puncture to look for M1 disease

- Computed tomography (CT) of chest and abdomen to check for a tumor

- Bone marrow aspiration to check for bone tumors. Sometimes the physician will perform a stem cell transplant

- Bone marrow biopsy

- Bone scan

The initial diagnosis of a tumor is made with a radiographic study (MRI or CT-). If CT was performed first, an MRI is usually performed as the images are often more detailed and may reveal previously undetected metastatic tumors in other locations of the brain. In addition, an MRI of the spine is usually performed. The AT/RT tumor often spreads to the spine. AT/RT is difficult to diagnose only from radiographic study; usually, a pathologist must perform a cytological or genetic analysis.

Examination of the cerebrospinal fluid is important (CSF), as one-third of patients will have intracranial dissemination with involvement of the CSF. Large tumor cells, eccentricity of the nuclei, and prominent nucleoli are consistent findings. Usually only a minority of AT/RT biopsies have rhabdoid cells, making diagnosis more difficult. Increasingly it is recommended that a genetic analysis be performed on the brain tumor, especially to find if a deletion in the INI1/hSNF5 gene is involved (appears to account for over 80% of the cases). The correct diagnosis of the tumor is critical to any protocol. Studies have shown that 8% to over 50% of AT/RT tumors are diagnosed incorrectly.

The histologic diagnosis of malignant rhabdoid tumour depends on identification of characteristic rhabdoid cells—large cells with eccentrically located nuclei and abundant, eosinophilic cytoplasm. However, the histology can be heterogeneous and the diagnosis of MRT can often be difficult. Misclassifications can occur.

In MRTs, the INI1 gene (SMARCB1)on chromosome 22q functions as a classic tumour suppressor gene. Inactivation of INI1 can occur via deletion, mutation, or acquired UPD.

In a recent study, SNP array karyotyping identified deletions or LOH of 22q in 49/51 rhabdoid tumours. Of these, 14 were copy neutral LOH (or acquired UPD), which is detectable by SNP array karyotyping, but not by FISH, cytogenetics, or arrayCGH. MLPA detected a single exon homozygous deletion in one sample that was below the resolution of the SNP array. SNP array karyotyping can be used to distinguish, for example, a medulloblastoma with an isochromosome 17q from a primary rhabdoid tumour with loss of 22q11.2. When indicated, molecular analysis of INI1 using MLPA and direct sequencing may then be employed. Once the tumour-associated changes are found, an analysis of germline DNA from the patient and the parents can be done to rule out an inherited or de novo germline mutation or deletion of INI1, so that appropriate recurrence risk assessments can be made.

Cytogenetics is the study of a tumor’s genetic make-up. Fluorescent "in situ" hybridization may be able to help locate a mutation or abnormality that may be allowing tumor growth. This technique has been shown to be useful in identifying some tumors and distinguishing two histologically similar tumors from each other (such as AT/RTs and PNETs). In particular, medulloblastmas/PNETs may possibly be differentiated cytogenetically from AT/RTs, as chromosomal deletions of 17p are relatively common with medulloblastoma and abnormalities of 22q11.2 are not seen. However, chromosomal 22 deletions are very comomon in AT/RTs.

In importance of the "hSNF5/INI1" gene located on chromosomal band 22q11.2 is highlighted, as the mutation’s presence is sufficient to change the diagnosis from a medulloblastoma or PNET to the more aggressive AT/RT classification. However, this mutation is not present in 100% of cases. Therefore, if the mutation is not present in an otherwise classic AT/RT immunohistochemical and morphologic pattern then the diagnosis remains an AT/RT.

Medulloblastomas affect just under two people per million per year, and affect children 10 times more than adults. Medulloblastoma is the second-most frequent brain tumor in children after pilocytic astrocytoma and the most common malignant brain tumor in children, comprising 14.5% of newly diagnosed cases. In adults, medulloblastoma is rare, comprising fewer than 2% of CNS malignancies.

The rate of new cases of childhood medulloblastoma is higher in males (62%) than females (38%), a feature which is not seen in adults. Medulloblastoma and other PNET`s are more prevalent in younger children than older children. About 40% of medulloblastoma patients are diagnosed before the age of five, 31% are between the ages of 5 and 9, 18.3% are between the ages of 10 and 14, and 12.7% are between the ages of 15 and 19.

The cumulative relative survival rate for all age groups and histology follow-up was 60%, 52%, and 47% at 5 years, 10 years, and 20 years, respectively. Patients diagnosed with a medulloblastoma or PNET are 50 times more likely to die than a matched member of the general population.

The most recent population-based (SEER) 5-year relative survival rates are 69% overall, but 72% in children (1–9 years) and 67% in adults (20+ years). The 20-year survival rate is 51% in children. Children and adults have different survival profiles, with adults faring worse than children only after the fourth year after diagnosis (after controlling for increased background mortality). Before the fourth year, survival probabilities are nearly identical. Longterm sequelae of standard treatment include hypothalamic-pituitary and thyroid dysfunction and intellectual impairment. The hormonal and intellectual deficits created by these therapies causes significant impairment of the survivors.

An X-ray computed tomography (CT) or magnetic resonance imaging (MRI) scan is necessary to characterize the anatomy of this tumor as to size, location, and its heter/homogeneity. However, final diagnosis of this tumor, like most tumors, relies on histopathologic examination (biopsy examination).

If resected, the surgeon will remove as much of this tumor as possible, without disturbing eloquent regions of the brain (speech/motor cortex) and other critical brain structure. Thereafter, treatment may include chemotherapy and radiation therapy of doses and types ranging based upon the patient's needs. Subsequent MRI examination are often necessary to monitor the resection cavity.

It is classified into two types, based on location in the body: peripheral PNET and CNS PNET.

Brain imaging (neuroimaging such as CT or MRI) is needed to determine the presence of brain metastases. In particular, contrast-enhanced MRI is the best method of diagnosing brain metastases, though detection is primarily done by CT. Biopsy is often recommended to confirm diagnosis.

The diagnosis of brain metastases typically follows a diagnosis of a systemic cancer. Occasionally, brain metastases will be diagnosed concurrently with a primary tumor or before the primary tumor is found.

Primitive neuroectodermal tumor (PNET) is a malignant (cancerous) neural crest tumor. It is a rare tumor, usually occurring in children and young adults under 25 years of age. The overall 5 year survival rate is about 53%.

It gets its name because the majority of the cells in the tumor are derived from neuroectoderm, but have not developed and differentiated in the way a normal neuron would, and so the cells appear "primitive".

PNET belongs to the Ewing family of tumors.

PXA is diagnosed through a combination of diagnostic processes:

- Initially, a doctor will interview the patient and do a clinical exam, which will include a neurological examination.

- A CT scan of the brain, and/or an MRI scan of the brain and spine, will be performed. A special dye may be injected into a vein before these scans to provide contrast and make tumors easier to see.

- For children experiencing seizures, an EEG might be part of the diagnostic process (the goal being to record the brain's electrical activity in order to identify and localize seizure activity).

- Finally, a biopsy of the tumor, taken through a needle during a simple surgical procedure, helps to confirm the diagnosis.

With treatment, pleomorphic xanthoastrocytomas are associated with a high rate of cure.

- Grade II pleomorphic xanthoastrocytomas are known to progress towards grade II tumors, which are more likely to recur after surgical removal.

- Grade III anaplastic pleomorphic xanthoastrocytomas may evolve and show signs of anaplasia, according to evidence in the medical literature.

The prognosis for brain metastases is variable. It depends on the type of primary cancer, the age of the patient, the absence or presence of extracranial metastases, and the number of metastatic sites in the brain. For patients who do not undergo treatment the average survival is between one and two months. However, in some patients, such as those with no extracranial metastases, those who are younger than 65, and those with a single site of metastasis in the brain only, prognosis is much better, with median survival rates of up to 13.5 months. Because brain metastasis can originate from various different primary cancers, the Karnofsky performance score is used for a more specific prognosis.

Many types of blastoma have been linked to a mutation in tumor suppressor genes. For example, pleuropulmonary blastomas have been linked to a mutation of the coding for p53. However, the mutation which allows proliferation of incompletely differentiated cells can vary from patient to patient and a mutation can alter the prognosis. In the case of retinoblastoma, patients carry a visibly abnormal karyotype, with a loss of function mutation on a specific band of chromosome 13. This recessive deletion on the rb gene is also associated with other cancer types and must be present on both alleles, for a normal cell to progress towards malignancy.

Treatment options include surgery, radiotherapy, radiosurgery, and chemotherapy.

The infiltrating growth of microscopic tentacles in fibrillary astrocytomas makes complete surgical removal difficult or impossible without injuring brain tissue needed for normal neurological function. However, surgery can still reduce or control tumor size. Possible side effects of surgical intervention include brain swelling, which can be treated with steroids, and epileptic seizures. Complete surgical excision of low grade tumors is associated with a good prognosis. However, the tumor may recur if the resection is incomplete, in which case further surgery or the use of other therapies may be required.

Standard radiotherapy for fibrillary astrocytoma requires from ten to thirty sessions, depending on the sub-type of the tumor, and may sometimes be performed after surgical resection to improve outcomes and survival rates. Side effects include the possibility of local inflammation, leading to headaches, which can be treated with oral medication. Radiosurgery uses computer modelling to focus minimal radiation doses at the exact location of the tumor, while minimizing the dose to the surrounding healthy brain tissue. Radiosurgery may be a complementary treatment after regular surgery, or it may represent the primary treatment technique.

Although chemotherapy for fibrillary astrocytoma improve overall survival, it is effective only in about 20% of cases. Researchers are currently investigating a number of promising new treatment techniques including gene therapy, immunotherapy, and novel chemotherapies.

A blastoma is a type of cancer, more common in children, that is caused by malignancies in precursor cells, often called blasts. Examples are nephroblastoma, medulloblastoma and retinoblastoma. The suffix "-blastoma" is used to imply a tumor of primitive, incompletely differentiated (or precursor) cells, e.g., chondroblastoma is composed of cells resembling the precursor of chondrocytes.

Medical imaging plays a central role in the diagnosis of brain tumors. Early imaging methods – invasive and sometimes dangerous – such as pneumoencephalography and cerebral angiography have been abandoned in favor of non-invasive, high-resolution techniques, especially magnetic resonance imaging (MRI) and computed tomography (CT) scans. Neoplasms will often show as differently colored masses (also referred to as processes) in CT or MRI results.

- Benign brain tumors often show up as hypodense (darker than brain tissue) mass lesions on CT scans. On MRI, they appear either hypodense or isointense (same intensity as brain tissue) on T1-weighted scans, or hyperintense (brighter than brain tissue) on T2-weighted MRI, although the appearance is variable.

- Contrast agent uptake, sometimes in characteristic patterns, can be demonstrated on either CT or MRI scans in most malignant primary and metastatic brain tumors.

- Pressure areas where the brain tissue has been compressed by a tumor also appear hyperintense on T2-weighted scans and might indicate the presence a diffuse neoplasm due to an unclear outline. Swelling around the tumor known as "peritumoral edema" can also show a similar result.

This is because these tumors disrupt the normal functioning of the BBB and lead to an increase in its permeability. However, it is not possible to diagnose high- versus low-grade gliomas based on enhancement pattern alone.

The definitive diagnosis of brain tumor can only be confirmed by histological examination of tumor tissue samples obtained either by means of brain biopsy or open surgery. The histological examination is essential for determining the appropriate treatment and the correct prognosis. This examination, performed by a pathologist, typically has three stages: interoperative examination of fresh tissue, preliminary microscopic examination of prepared tissues, and follow-up examination of prepared tissues after immunohistochemical staining or genetic analysis.

The prognosis of brain cancer depends on the type of cancer diagnosed. Medulloblastoma has a good prognosis with chemotherapy, radiotherapy, and surgical resection while glioblastoma multiforme has a median survival of only 12 months even with aggressive chemoradiotherapy and surgery. Brainstem gliomas have the poorest prognosis of any form of brain cancer, with most patients dying within one year, even with therapy that typically consists of radiation to the tumor along with corticosteroids. However, one type, focal brainstem gliomas in children, seems open to exceptional prognosis and long-term survival has frequently been reported.

The standard treatment for DIPG is 6 weeks of radiation therapy, which often dramatically improves symptoms. However, symptoms usually recur after 6 to 9 months and progress rapidly.

Ependymomas make up about 5% of adult intracranial gliomas and up to 10% of childhood tumors of the central nervous system (CNS). Their occurrence seems to peak at age 5 years and then again at age 35. They develop from cells that line both the hollow cavities of the brain and the canal containing the spinal cord, but they usually arise from the floor of the fourth ventricle, situated in the lower back portion of the brain, where they may produce headache, nausea and vomiting by obstructing the flow of cerebrospinal fluid. This obstruction may also cause hydrocephalus. They may also arise in the spinal cord, conus medullaris and supratentorial locations. Other symptoms can include (but are not limited to): loss of appetite, difficulty sleeping, temporary inability to distinguish colors, uncontrollable twitching, seeing vertical or horizontal lines when in bright light, and temporary memory loss. It should be remembered that these symptoms also are prevalent in many other illnesses not associated with ependymoma.

About 10% of ependymomas are benign myxopapillary ependymoma (MPE). MPE is a localized and slow-growing low-grade tumor, which originates almost exclusively from the lumbosacral nervous tissue of young patients. On the other hand, it is the most common tumor of the lumbosacral canal comprising about 90% of all tumoral lesions in this region.

Although some ependymomas are of a more anaplastic and malignant type, most of them are not anaplastic. Well-differentiated ependymomas are usually treated with surgery. For other ependymomas, total surgical removal is the preferred treatment in addition to radiation therapy. The malignant (anaplastic) varieties of this tumor, malignant ependymoma and the ependymoblastoma, are treated similarly to medulloblastoma but the prognosis is much less favorable. Malignant ependymomas may be treated with a combination of radiation therapy and chemotherapy. Ependymoblastomas, which occur in infants and children younger than 5 years of age, may spread through the cerebrospinal fluid and usually require radiation therapy. The subependymoma, a variant of the ependymoma, is apt to arise in the fourth ventricle but may occur in the septum pellucidum and the cervical spinal cord. It usually affects people over 40 years of age and more often affects men than women.

Extraspinal ependymoma (EEP), also known as extradural ependymoma, may be an unusual form of teratoma or may be confused with a sacrococcygeal teratoma.

Surgery to attempt tumour removal is usually not possible or advisable for DIPG. By nature, these tumours invade diffusely throughout the brain stem, growing between normal nerve cells. Aggressive surgery would cause severe damage to neural structures vital for arm and leg movement, eye movement, swallowing, breathing, and even consciousness.

A neurosurgically performed brain-stem biopsy for immunotyping of diffuse intrinsic pontine glioma has served a limited recent role in experimental clinical studies and treatment trials. This however is not the current standard of care as it presents considerable risk given the biopsy location, and thus is appropriately performed in the context of participation in an ongoing clinical treatment trial.

Pontine biopsy is in no way a therapeutic or curative surgery, and the risks (potentially catastrophic and fatal) are only outweighed when the diagnosis is uncertain (extremely unusual) or the patient is enrolled in an approved clinical trial.

Fibrillary astrocytomas arise from neoplastic astrocytes, a type of glial cell found in the central nervous system. They may occur anywhere in the brain, or even in the spinal cord, but are most commonly found in the cerebral hemispheres. As the alternative name of "diffuse astrocytoma" implies, the outline of the tumour is not clearly visible in scans, because the borders of the neoplasm tend to send out tiny microscopic fibrillary tentacles that spread into the surrounding brain tissue. These tentacles intermingle with healthy brain cells, making complete surgical removal difficult. However, they are low grade tumors, with a slow rate of growth, so that patients commonly survive longer than those with otherwise similar types of brain tumour, such as glioblastoma multiforme.

The prognosis for gliomatosis cerebri is generally poor. Surgery is not practical considering the extent of the disease, standard chemotherapy (nitrosourea) has been unsuccessful, and while brain irradiation can stabilize or improve neurologic function in some patients, its impact on survival has yet to be proven.

In 2014, Weill Cornell Brain and Spine Center launched an international registry for Gliomatosis Cerebri, where tissue samples can be stored for genomic study.

Criteria for CSF abnormalities:

- Increased opening pressure (> 200mm of H2O)

- Increased Leukocytes (>4/mm3)

- Elevated protein (>50 mg/dL)

- Decreased glucose (<60 mg/dL)

Tumor Markers:

- Carcinoembryonic antigin (CEA)

- alpha-fetoprotein

- beta-human chorionic gonadotropin

- carbohydrate antigen19-9

- creatine-kinase BB

- isoenzyme

- tissue polypeptide antigen

- beta2-microglobulin,

- beta-glucoronidase

- lactate dehydrogenase isoenzyme-5

- vascular endothelial growth factor

These markers can be good indirect indicator of NM but most are not sensitive enough to improve cytogical diagnosis.

Avoiding false-negative

- Draw CSF from symptomatic or radiographically demonstrated disease.

- Draw large amount of CSF (>10.5mL).

- Don't delay processing of specimen.

- Obtain at least 2 samples. The first sample has diagnostic sensitivity of 54% but with repeated sampling, diagnostic sensitivity is increased to 91%.

Ideal procedure for diagnosis:

Lumbar puntures --> cranial MRI --> spinal MRI --> radioisotope CSF flow --> ventricular or lateral cervical spine CSF analysis (if previous step yields no definitive answer)